From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 30 Nov 2017 15:20:19 +0000 (+0000)
Subject: JAL-2850 improved use of htsjdk api to read contig info
X-Git-Tag: Release_2_11_0~96
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=946a0619168de3fbe9858401d13bcd1981d0a0df

JAL-2850 improved use of htsjdk api to read contig info
---

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 2a3ddef..a85802a 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -32,11 +32,12 @@ import java.util.TreeMap;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
+import htsjdk.samtools.SAMException;
+import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.VCFContigHeaderLine;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
 import htsjdk.variant.vcf.VCFHeaderLineCount;
@@ -147,6 +148,11 @@ public class VCFLoader
   private VCFHeader header;
 
   /*
+   * a Dictionary of contigs (if present) referenced in the VCF file
+   */
+  private SAMSequenceDictionary dictionary;
+
+  /*
    * the position (0...) of field in each block of
    * CSQ (consequence) data (if declared in the VCF INFO header for CSQ)
    * see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
@@ -234,6 +240,14 @@ public class VCFLoader
 
       header = reader.getFileHeader();
 
+      try
+      {
+        dictionary = header.getSequenceDictionary();
+      } catch (SAMException e)
+      {
+        // ignore - thrown if any contig line lacks length info
+      }
+
       sourceId = filePath;
 
       saveMetadata(sourceId);
@@ -294,6 +308,8 @@ public class VCFLoader
           // ignore
         }
       }
+      header = null;
+      dictionary = null;
     }
   }
 
@@ -543,17 +559,27 @@ public class VCFLoader
     /*
      * simplest case: sequence has id and length matching a VCF contig
      */
+    VCFMap vcfMap = null;
+    if (dictionary != null)
+    {
+      vcfMap = getContigMap(seq);
+    }
+    if (vcfMap != null)
+    {
+      return vcfMap;
+    }
+
+    /*
+     * otherwise, map to VCF from chromosomal coordinates 
+     * of the sequence (if known)
+     */
     GeneLociI seqCoords = seq.getGeneLoci();
     if (seqCoords == null)
     {
-      VCFMap map = getContigMap(seq);
-      if (map == null)
-      {
-        Cache.log.warn(String.format(
-                "Can't query VCF for %s as chromosome coordinates not known",
-                seq.getName()));
-      }
-      return map;
+      Cache.log.warn(String.format(
+              "Can't query VCF for %s as chromosome coordinates not known",
+              seq.getName()));
+      return null;
     }
 
     String species = seqCoords.getSpeciesId();
@@ -619,8 +645,8 @@ public class VCFLoader
 
   /**
    * If the sequence id matches a contig declared in the VCF file, and the
-   * sequence matches the contig length, then returns a 1:1 map of the sequence to
-   * the contig, else returns null
+   * sequence length matches the contig length, then returns a 1:1 map of the
+   * sequence to the contig, else returns null
    * 
    * @param seq
    * @return
@@ -628,25 +654,17 @@ public class VCFLoader
   private VCFMap getContigMap(SequenceI seq)
   {
     String id = seq.getName();
-    for (VCFContigHeaderLine contig : header.getContigLines())
+    SAMSequenceRecord contig = dictionary.getSequence(id);
+    if (contig != null)
     {
-      if (contig.getID().equals(id))
+      int len = seq.getLength();
+      if (len == contig.getSequenceLength())
       {
-        /*
-         * have to construct a SAMSequenceRecord to
-         * read the contig 'length' field!
-         */
-        int len = seq.getLength();
-        SAMSequenceRecord ssr = contig.getSAMSequenceRecord();
-        if (len == ssr.getSequenceLength())
-        {
-          MapList map = new MapList(new int[] { 1, len },
-                  new int[]
-                  { 1, len }, 1, 1);
-          return new VCFMap(id, map);
-        }
+        MapList map = new MapList(new int[] { 1, len },
+                new int[]
+                { 1, len }, 1, 1);
+        return new VCFMap(id, map);
       }
-
     }
     return null;
   }